- Volume 56, Issue 1, 2006

The taxonomic status of two bacterial strains isolated from human blood was characterized using a polyphasic approach. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV, short-chain mycolic acids that co-migrated with those extracted from members of the genus Williamsia and that produce C16 : 0 and C18 : 0 fatty acids on pyrolysis GC, and dihydrogenated menaquinone with nine isoprene units as the predominant isoprenologue. The generic assignment was confirmed by 16S rRNA gene sequencing. Comparative analysis of the 16S rRNA gene sequence showed that these isolates constitute a distinct phyletic line within the genus Williamsia, displaying 96·2 and 97·2 % sequence similarities to Williamsia muralis and Williamsia maris, respectively. The two isolates could be distinguished from the type strains of the latter species on the basis of several phenotypic traits. The genotypic and phenotypic data show that the strains merit classification as a novel species of Williamsia, for which the name Williamsia deligens sp. nov. is proposed, with type strain IMMIB RIV-956T (=DSM 44902T=CCUG 50873T).

Amycolatopsis orientalis DSM 43387, a clinical isolate from submandibular mycetoma tissue, is one of three plasmid-bearing strains of the genus Amycolatopsis. It degrades aromatic compounds such as m-hydroxybenzoate, but does not produce any antibiotics, in contrast to Amycolatopsis orientalis NBRC 12806T. Phylogenetic analysis based on a complete 16S rRNA gene sequence placed the strain in the clade of Amycolatopsis albidoflavus IMSNU 22139T, distant from the clade of A. orientalis NBRC 12806T. The strain showed low DNA–DNA hybridization values of 24·1 and 45·7 % with A. orientalis NBRC 12806T and A. albidoflavus DSM 44639T (=IMSNU 22139T), respectively. It could also be readily distinguished from A. orientalis NBRC 12806T and all species with validly published names classified in the genus Amycolatopsis, by using a combination of chemical and physiological markers such as utilization of lactose, degradation of xanthine, hypoxanthine, gelatin and casein and hydrolysis of Tween 80, indicating that it represents a novel species. Strain DSM 43387 could also be differentiated from A. orientalis NBRC 12806T and its nearest neighbour A. albidoflavus IMSNU 22139T on the basis of fatty acid and phospholipid profiles. Based on genotypic and phenotypic differences, the name Amycolatopsis benzoatilytica sp. nov. is proposed for strain DSM 43387 that was previously classified as Amycolatopsis orientalis. The type strain is AK 16/65T (=DSM 43387T=ATCC 55165T=IMRU 1389T).

A novel actinomycete, strain H647-1T, which was isolated from soil of Mt. Halla, Jeju Island, Republic of Korea, was subjected to phenotypic and genotypic characterization. The organism, which produces warty spore chains arranged in hooks or spirals on the aerial mycelium, was shown to have chemotaxonomic characteristics consistent with assignment to the genus Actinomadura. A comparative analysis of 16S rRNA gene sequences indicated that the organism formed a distinct clade within the evolutionary radiation of the family Thermomonosporaceae and that it was closely associated with members of the genus Actinomadura, but possessed a 22 nt extended loop between positions 453 and 479 of the 16S rRNA gene sequence (Escherichia coli numbering). A broad range of phenotypic and genetic data supported the suggestion that this organism represents a novel species of the genus Actinomadura, for which the name Actinomadura hallensis sp. nov. is proposed. The type strain is strain H647-1T (=IMSNU 50760T=KCTC 9992T=KCCM 42245T=NRRL B-24436T).

Two actinomycete strains, 32U-2T and 32U-4, were isolated from a prairie soil in Minnesota and subjected to characterization by means of polyphasic taxonomy. The 16S rRNA gene sequences were determined following PCR amplification and cloning. A phylogenetic analysis, based on comparative analysis of 16S rRNA gene sequences, indicated that the organisms consistently formed a well-separated, distinct sub-branch within the radiation of the genus Amycolatopsis of the family Pseudonocardiaceae. The levels of 16S rRNA sequence similarity between the isolates and the type strains of recognized Amycolatopsis species ranged from 94·1 to 97·9 %. The highest levels of sequence similarity were found between the isolates and Amycolatopsis coloradensis (97·6–97·9 %), Amycolatopsis alba and Amycolatopsis orientalis (97·3–97·6 %) and Amycolatopsis lurida (97·2–97·5 %). Chemotaxonomic characteristics supported the phylogenetic relationships between the organisms and members of the genus Amycolatopsis. However, a broad range of phenotypic and genetic data revealed that the isolates should be classified as novel species of the genus Amycolatopsis, for which the name Amycolatopsis minnesotensis sp. nov. is proposed. The type strain is 32U-2T (=KCCM 42246T=NRRL B-24435T).

Gram-positive, rod- or coccoid-shaped bacterial strains KSL-17T, KSL-18 and KSL-19 were isolated from an alkaline soil in Korea. They were subjected to analysis using polyphasic taxonomy. Strains KSL-17T, KSL-18 and KSL-19 grew optimally at pH 8·0 and 28 °C and in the presence of 0·5 % (w/v) NaCl. They were characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and iso-C16 : 0 as the major fatty acid. Their DNA G+C contents were in the range 74·6–74·8 mol%. Strains KSL-17T, KSL-18 and KSL-19 were identical in terms of their 16S rRNA gene sequences and exhibited a mean level of DNA–DNA relatedness of 85–90 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains KSL-17T, KSL-18 and KSL-19 formed a distinct phylogenetic lineage within the genus Nocardioides. The levels of 16S rRNA gene sequence similarity between the three strains and the type strains of Nocardioides species were in the range 92·6–95·2 %. On the basis of phenotypic, genetic and phylogenetic data, strains KSL-17T (=KCTC 19039T=DSM 16315T), KSL-18 and KSL-19 should be classified as members of a novel species of the genus Nocardioides, for which the name Nocardioides lentus sp. nov. is proposed.

Three xylan-degrading actinobacterial strains were isolated from different sampling sites in the Roman catacombs of Domitilla and San Callisto. The organisms showed morphological and chemotaxonomic properties such as peptidoglycan type A4α, l-lys–l-thr–d-Glu; whole-cell sugars (glucose, mannose and galactose); octa-, hexa- and tetrahydrogenated menaquinones with nine isoprene units; phosphatidylglycerol and diphosphatidylglycerol as the major phospholipids; anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0 as the predominant fatty acids; and a DNA G+C content of 72 mol%. These features are consistent with affiliation of these isolates to the genus Myceligenerans. The three isolates shared a 16S rRNA gene similarity of 99·9 % and were most closely related to Myceligenerans xiligouense DSM 15700T (97·9 % sequence similarity). The low level of DNA–DNA relatedness (about 14 %) and the differences in phenotypic characteristics between the novel strains and M. xiligouense DSM 15700T justify the proposal of a novel species of the genus Myceligenerans, Myceligenerans crystallogenes sp. nov., with CD12E2-27T (=HKI 0369T=DSM 17134T=NCIMB 14061T=VTT E-032285T) as the type strain.

Two methanogenic strains, 8AcT and 6Ac, were isolated from an upflow anaerobic sludge blanket reactor treating beer-manufacture wastewater in Beijing, China. Cells of strains 8AcT and 6Ac were rod-shaped (0·8–1·0×3–5 μm) and non-motile, occurring singly or in pairs; however, at high cell density the cells were arranged in long chains within a common sheath. The two strains used acetate exclusively for growth and methane production. The specific growth rate of strain 8AcT was 0·030 h−1 when growing in acetate (20 mM) at 37 °C. The temperature range for growth was 25–45 °C, with the fastest growth at 34–37 °C. The pH range for growth and methane production was 6·5–9·0, with the fastest growth at pH 7·2–7·6. The G+C content of genomic DNA of strain 8AcT was 55·7 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that the novel strains clustered with Methanosaeta species; the 16S rRNA gene sequence similarities between strain 8AcT and Methanosaeta concilii DSM 3013 and ‘Methanosaeta thermophila’ DSM 6194 were 92·5 and 87·3 %, respectively. The sequence similarity levels of mcrA, the gene encoding the α-subunit of methyl-coenzyme M reductase, and of the deduced amino acids of mcrA, between strain 8AcT and Methanosaeta concilii DSM 3671T were 36 and 78·9 %, respectively. Based on the phylogenetic and phenotypic analyses, the novel species Methanosaeta harundinacea sp. nov. is proposed, with strain 8AcT (=JCM 13211T=CGMCC 1.5026T) as the type strain.

A strictly anaerobic, propionate-producing bacterial strain (WB4T) isolated from rice plant residue in anoxic rice-field soil in Japan was characterized phenotypically and phylogenetically. Cells were Gram-negative, non-motile, non-spore-forming, short rods. The strain utilized various sugars and produced propionate and acetate as major fermentation products with a small amount of succinate. The optimum growth temperature was 30 °C. Oxidase, catalase and nitrate-reducing activities were negative. The major cellular fatty acids were anteiso-C15 : 0, C15 : 0 and anteiso-C17 : 0 3-OH. Menaquinone MK-8(H4) was the major respiratory quinone. The genomic DNA G+C content was 39·3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain in the phylum ‘Bacteroidetes’. The closest relative to strain WB4T was an environmental clone from water contaminated with equine manure (sequence similarity of 99·7 %) and the strain formed a distinct cluster with other environmental clones mainly from freshwater sediments. The closest recognized species were members of the genus Dysgonomonas, with 16S rRNA gene sequence similarities of 90·9–89·8 %. Bacteroides merdae was the next closest recognized species (similarity of 88·7 % to the type strain). Given that the ecological, physiological and chemotaxonomic characteristics of strain WB4T were different from those of any related species, a new genus and species Paludibacter propionicigenes gen. nov., sp. nov., is proposed to accommodate it. The type strain is WB4T (=JCM 13257T=DSM 17365T).

A Gram-negative, non-spore-forming and rod-shaped gliding bacterium, designated strain SMK-19T, was isolated from a tidal flat sediment of the Yellow Sea, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain SMK-19T grew optimally at 37 °C, in the presence of 2–3 % (w/v) NaCl and at pH 7·0–8·0. It contained MK-6 as the predominant menaquinone, and iso-C17 : 0 3-OH and iso-C15 : 0 as the major fatty acids. Major polar lipids were phosphatidylethanolamine, unidentified phospholipids and an amino-group-containing lipid that is ninhydrin-positive. The DNA G+C content was 36·0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that strain SMK-19T formed a distinct evolutionary lineage within the family Flavobacteriaceae. The 16S rRNA gene sequence of strain SMK-19T exhibited similarity values of <94·4 % to those of other members of the family Flavobacteriaceae. Strain SMK-19T was distinguished from phylogenetically related genera by differences in several phenotypic properties. On the basis of phenotypic, phylogenetic and chemotaxonomic data, SMK-19T (=KCTC 12390T=DSM 17196T) was classified at the type strain of a novel genus and species, Gaetbulimicrobium brevivitae gen. nov., sp. nov.

During studies of the microbiota of human faeces, five strains of Gram-negative anaerobic rods were isolated following growth in a polyamine-deficient medium. These strains belonged to the genus Bacteroides on the basis of 16S rRNA gene sequence data. 16S rRNA gene sequence similarity between one of the strains, 341T, and recognized species within the genus Bacteroides was <95 %. The DNA G+C content (44 mol%) and major fatty acid composition (anteiso-C15 : 0, 32·0 %) supported the affiliation of strain 341T to the genus Bacteroides. Biochemical tests and DNA–DNA hybridization analysis demonstrated that strain 341T was distinct from Bacteroides uniformis and Bacteroides helcogenes, to which it was related most closely. On the basis of these data, a novel Bacteroides species, Bacteroides intestinalis sp. nov., is proposed with strain 341T (=JCM 13265T=DSM 17393T) as the type strain.

The taxonomic position of three novel, marine, heterotrophic, aerobic, pigmented, gliding bacteria, isolated from the green alga Ulva fenestrata in the Sea of Japan, was determined. 16S rRNA gene sequence analysis revealed that the strains belong to the genus Arenibacter. The results of DNA–DNA hybridization experiments supported by phenotypic and chemotaxonomic data showed that the isolates represent a novel species of the genus Arenibacter, for which the name Arenibacter palladensis sp. nov. is proposed. The type strain is KMM 3961T (=LMG 21972T=CIP 108849T).

Two marine, heterotrophic, aerobic, yellow-pigmented, agarolytic bacterial strains that are motile by means of gliding were isolated from the green alga Acrosiphonia sonderi and from sea water. Comparative 16S rRNA gene sequence analysis revealed an affiliation between the strains studied and the genus Formosa, a member of the family Flavobacteriaceae. The level of sequence similarity between strain KMM 3901T and Formosa algae KMM 3553T was 99·1 %. The results of DNA–DNA hybridization experiments and phenotypic analysis indicated that the strains represent a novel species of the genus Formosa, for which the name Formosa agariphila sp. nov. is proposed, with KMM 3901T (=KCTC 12365T=LMG 23005T=DSM 15362T) as the type strain. The description of the genus Formosa is emended with newly obtained data.

Members of the phylum ‘Bacteroidetes’ are important heterotrophs involved in cycling organic carbon in aquatic habitats. Their diversity has been studied by molecular methods in both freshwater and marine habitats and many novel genera and species within this phylum have been characterized in recent years. In this study, we examined the diversity of members of the ‘Bacteroidetes’ that could be readily isolated on solid media from river epilithon and coastal sea water. Most (93 %) of the 55 isolates confirmed as members of the ‘Bacteroidetes’ and examined by phylogenetic analysis of 16S rRNA gene sequences belonged to the Flavobacteriaceae. Furthermore, most (62 %) of these were almost certainly members of the genus Flavobacterium and all but one were from river epilithon. Conversely, the sea-water isolates were more widely distributed in clades containing other genera. Some of the isolates were deep-branching within phylogenetic trees and so could not be assigned to putative genera. Two of these deep-branching isolates were characterized by polyphasic taxonomy and are proposed as novel species within two new genera of the family Flavobacteriaceae. These are Epilithonimonas tenax gen. nov., sp. nov. (type strain EP105T=NCIMB 14026T=DSM 16811T) and Persicivirga xylanidelens gen. nov., sp. nov. (type strain SW256T=NCIMB 14027T=DSM 16809T).

A bacterial strain, UST030701-156T, was isolated from a marine sponge in the Bahamas. Strain UST030701-156T was orange-pigmented, Gram-negative, rod-shaped with tapered ends, slowly motile by gliding and strictly aerobic. The predominant fatty acids were a15 : 0, i15 : 0, i15 : 0 3-OH, i17 : 0 3-OH, i17 : 1ω9c and summed feature 3, comprising i15 : 0 2-OH and/or 16 : 1ω7c. MK-6 was the only respiratory quinone. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences placed UST030701-156T within a distinct lineage in the family Flavobacteriaceae, with 93·3 % sequence similarity to the nearest neighbour, Nonlabens tegetincola. The DNA G+C content of UST030701-156T was 41·0 mol% and was much higher than that of N. tegetincola (33·6 mol%). Strain UST030701-156T can be distinguished from other members of the Flavobacteriaceae by means of a number of chemotaxonomic and phenotypic characteristics. It is proposed, therefore, that UST030701-156T represents a novel taxon designated Stenothermobacter spongiae gen. nov., sp. nov. The type strain is UST030701-156T (=NRRL B-41138T=JCM 13191T). Carbon-source utilization by N. tegetincola was re-examined and an emended description is therefore included.

A Gram-negative, non-motile, non-spore-forming and rod-shaped bacterial strain, DSW-6T, was isolated from sea water and subjected to a polyphasic study. Strain DSW-6T grew optimally at 25 °C, in the presence of 2 % (w/v) NaCl and at pH 7·0–8·0. It was characterized chemotaxonomically as having MK-6 as the predominant menaquinone and iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and C15 : 0 as the major fatty acids (>10 % of total fatty acids). Major polar lipids were phosphatidylethanolamine, unidentified phospholipids and amino-group-containing lipids that are ninhydrin-positive. The DNA G+C content was 36·9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DSW-6T forms an independent line of descent within the family Flavobacteriaceae. The 16S rRNA gene sequence of strain DSW-6T exhibited similarity values of less than 94·7 % to the sequences of other members of the family Flavobacteriaceae. Strain DSW-6T could be distinguished from other phylogenetically related genera by differences in several phenotypic properties. Therefore, in view of the combined phenotypic and phylogenetic data, it is proposed that strain DSW-6T (=KCTC 12402T=DSM 17205T) represents a novel genus and species, Donghaeana dokdonensis gen. nov., sp. nov.

A Gram-negative bacterium, designated strain LMG 22510T, was isolated from water of a pharmaceutical company steam generator. The cells had a ring-like and horseshoe-shaped morphology and possessed gliding motility. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain was a member of the Flexibacter group within the phylum ‘Bacteroidetes’; its nearest neighbour was Spirosoma linguale (88·8 % sequence similarity). DNA base content, fatty acid composition and biochemical characteristics were determined. Genotypic and phenotypic data indicated that strain LMG 22510T could not be assigned to any recognized genus; therefore, a novel genus and species is proposed, Larkinella insperata gen. nov., sp. nov., with LMG 22510T (=NCIMB 14103T) as the type strain.